FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.

GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)

GlycospectrumScan - an analytical tool independent of MS-platform that accurately identifies and assigns the oligosaccharide heterogeneity on glycopeptides from MS data of a mixture of peptides and glycopeptides (Reference)

Glycoviewer - a visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG) (Reference)

Other tools for MS data (vizualisation, quantitation, analysis, etc.)

HCD/CID spectra merger - a tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines